* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘rxode2’ ...
** package ‘rxode2’ successfully unpacked and MD5 sums checked
** using staged installation
R version 4.4.0 Patched (2024-05-06 r86527) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> ## This is only for rxode2
> for (f in c("inst/include/rxode2_RcppExports.h", "src/RcppExports.cpp")) {
+ l <- readLines(f)
+ w <- which(regexpr("^[#]include <RcppArmadillo.h>", l) != -1)
+ if (length(w) > 0) {
+ l <- l[-w]
+ }
+ w <- which(regexpr("^[#]define R_STRICT_HEADERS", l) != -1)
+ if (length(w) > 0) {
+ l <- l[-w]
+ }
+ l <- c("#define R_STRICT_HEADERS",
+ "#include <RcppArmadillo.h>",
+ l)
+ file.out <- file(f, "wb")
+ writeLines(l, file.out)
+ close(file.out)
+ }
>
> l <- readLines("R/RcppExports.R")
> w <- which(regexpr("# Register entry points", l, fixed=TRUE) != -1)
> if (length(w) >= 1) {
+ w <- w[1]
+ l <- l[seq(1, w-1)]
+ RcppExports.R <- file("R/RcppExports.R", "wb")
+ writeLines(l, RcppExports.R)
+ close(RcppExports.R)
+ }
>
> .in <- suppressWarnings(readLines("src/Makevars.in"))
> .in <- gsub("@ARMA@", file.path(find.package("RcppArmadillo"),"include"), .in)
> .in <- gsub("@BH@", file.path(find.package("BH"),"include"), .in)
> .in <- gsub("@RCPP@", file.path(find.package("Rcpp"),"include"), .in)
>
>
>
> if (.Platform$OS.type == "windows" && !file.exists("src/Makevars.win")) {
+ .in <- gsub("@CXX14STD@", "-std=c++1y", .in)
+ file.out <- file("src/Makevars.win", "wb")
+ writeLines(gsub("@ISYSTEM@", "I", .in),
+ file.out)
+ close(file.out)
+ } else {
+ .in <- gsub("@CXX14STD@", "-std=gnu++14", .in)
+ file.out <- file("src/Makevars", "wb")
+ writeLines(gsub("@ISYSTEM@", "isystem", .in),
+ file.out)
+ close(file.out)
+ }
>
> if (file.exists("man/reexports.Rd")) {
+ l <- readLines("man/reexports.Rd")
+ if (!any(regexpr("[\\]value", l) != -1)) {
+ l <- c(l, "\\value{ Inherited from parent routine }")
+ file.out <- file("man/reexports.Rd", "wb")
+ writeLines(l, file.out)
+ close(file.out)
+ }
+ }
>
>
> unlink("R/rxode2_md5.R")
>
> cpp <- list.files("src", pattern = ".(c|h|cpp|f)$")
> include <- list.files("inst/include")
> #Rfiles <- list.files("R/", pattern = ".R")
>
> cmd <- file.path(R.home("bin"), "R")
> args <- c("CMD", "config")
>
> md5 <- digest::digest(c(lapply(c(paste0("src/", cpp),
+ paste0("inst/include/", include)#,
+ #paste0("R/", Rfiles)
+ ), digest::digest, file = TRUE),
+ rxode2parse::rxode2parseMd5(),
+ rxode2random::rxode2randomMd5(),
+ ## vapply(c("BLAS_LIBS", "CC", "CFLAGS", "CPICFLAGS",
+ ## "CXX", "CXXFLAGS", "CXXPICFLAGS",
+ ## "CXX11", "CXX11STD", "CXX11FLAGS", "CXX11PICFLAGS",
+ ## "CXX14", "CXX14STD", "CXX14FLAGS", "CXX14PICFLAGS",
+ ## "CXX17", "CXX17STD", "CXX17FLAGS", "CXX17PICFLAGS",
+ ## "CXX20", "CXX20STD", "CXX20FLAGS", "CXX20PICFLAGS",
+ ## "FC", "FFLAGS", "FCFLAGS", "FPICFLAGS"),
+ ## function(cfg) {
+ ## rawToChar(sys::exec_internal(cmd, c(args, cfg))$stdout)
+ ## }, character(1)
+ ## ),
+ ""
+ ))
> unlink("R/rxode2_md5.R")
> md5file <- file("R/rxode2_md5.R", "wb")
> writeLines(sprintf("rxode2.md5 <- \"%s\"\n", md5), md5file)
> close(md5file)
>
> l <- readLines(file.path(system.file(package="rxode2parse"), "include", "sbuf.c"))
>
> sbuf.c <- file("src/sbuf.c", "wb")
> .w <- which(regexpr(" *extern +SEXP +_goodFuns; *", l) != -1)
> l <- l[-seq(.w, length(l))]
> writeLines(l, sbuf.c)
> close(sbuf.c)
>
> proc.time()
user system elapsed
0.631 0.086 0.723
--------[begin src/Makevars]--------
# -*- mode: makefile-gmake -*-
BH=/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include
################################################################################
## Package library flags.
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS)
# Release options
PKG_CFLAGS = -D_isrxode2_
PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"$(BH)"
--------[end src/Makevars]--------
--------[begin R/RxODE_md5.R]--------
rxode2.md5 <- "e494a54d1c17136ec72b60d73c1bfb6f"
--------[end R/RxODE_md5.R]--------
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-24) 13.2.0’
using Fortran compiler: ‘GNU Fortran (Debian 13.2.0-24) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-24) 13.2.0’
make[1]: Entering directory '/tmp/RtmpLdTs3U/R.INSTALL2ecac55de2ade2/rxode2/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c approx.c -o approx.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c boost.cpp -o boost.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c box.c -o box.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c call_dvode.c -o call_dvode.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cfode.c -o cfode.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cfode_static.c -o cfode_static.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c common.c -o common.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c corfailure.c -o corfailure.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c correction.c -o correction.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c daxpy.c -o daxpy.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ddot.c -o ddot.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dgefa.c -o dgefa.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dgesl.c -o dgesl.o
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c dgpadm.f -o dgpadm.o
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c dlsoda.f -o dlsoda.o
dlsoda.f:2536:72:
2536 | IF (JT .GE. 4) LENWM = (2*ML + MU + 1)*N + 2
| ^
Warning: ‘ml’ may be used uninitialized [-Wmaybe-uninitialized]
dlsoda.f:2407:32:
2407 | 1 LENIW, LENRW, LENWM, ML, MORD, MU, MXHNL0, MXSTP0
| ^
note: ‘ml’ was declared here
dlsoda.f:2536:72:
2536 | IF (JT .GE. 4) LENWM = (2*ML + MU + 1)*N + 2
| ^
Warning: ‘mu’ may be used uninitialized [-Wmaybe-uninitialized]
dlsoda.f:2407:42:
2407 | 1 LENIW, LENRW, LENWM, ML, MORD, MU, MXHNL0, MXSTP0
| ^
note: ‘mu’ was declared here
dlsoda.f:2615:29:
2615 | IF (H0 .NE. 0.0D0 .AND. (T + H0 - TCRIT)*H0 .GT. 0.0D0)
| ^
Warning: ‘h0’ may be used uninitialized [-Wmaybe-uninitialized]
dlsoda.f:2412:48:
2412 | DOUBLE PRECISION ATOLI, AYI, BIG, EWTI, H0, HMAX, HMX, RH, RTOLI,
| ^
note: ‘h0’ was declared here
dlsoda.f:2851:72:
2851 | IHIT = ABS(TN - TCRIT) .LE. 100.0D0*UROUND*HMX
| ^
Warning: ‘tcrit’ may be used uninitialized [-Wmaybe-uninitialized]
dlsoda.f:2413:14:
2413 | 1 TCRIT, TDIST, TNEXT, TOL, TOLSF, TP, SIZE, SUM, W0
| ^
note: ‘tcrit’ was declared here
dlsoda.f:2874:10:
2874 | IF (IHIT) T = TCRIT
| ^
Warning: ‘ihit’ may be used uninitialized [-Wmaybe-uninitialized]
dlsoda.f:2415:18:
2415 | LOGICAL IHIT
| ^
note: ‘ihit’ was declared here
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dop853.c -o dop853.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dscal.c -o dscal.o
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c dsphiv.f -o dsphiv.o
dsphiv.f:270:72:
270 | wsp(iphih+mbrkdwn+1) = hj1j*wsp(iphih+2*mx+mbrkdwn-1)
| ^
Warning: ‘hj1j’ may be used uninitialized [-Wmaybe-uninitialized]
dsphiv.f:125:35:
125 | . avnorm, hj1j, hjj, SQR1
| ^
note: ‘hj1j’ was declared here
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c etTran.cpp -o etTran.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c expandGrid.cpp -o expandGrid.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c expm.cpp -o expm.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fnorm.c -o fnorm.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c forder.cpp -o forder.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c handle_evid.c -o handle_evid.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c idamax.c -o idamax.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c intdy.c -o intdy.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lsoda.c -o lsoda.o
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c matexp.f -o matexp.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c matexp_HM98.c -o matexp_HM98.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c methodswitch.c -o methodswitch.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c nearPD.cpp -o nearPD.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c omegaChol.c -o omegaChol.o
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c opkda2.f -o opkda2.o
opkda2.f:650:28:
650 | INTEGER FUNCTION IXSAV (IPAR, IVALUE, ISET)
| ^
Warning: ‘__result_ixsav’ may be used uninitialized [-Wmaybe-uninitialized]
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c orderswitch.c -o orderswitch.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c par_solve.cpp -o par_solve.o
In file included from par_solve.cpp:13:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include/rxode2parseGetTime.h: In function ‘int handleInfusionStartRm(int*, int*, double*, int*, rx_solve*, rx_solving_options*, rx_solving_options_ind*)’:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include/rxode2parseGetTime.h:223:9: warning: unused variable ‘curEvid’ [-Wunused-variable]
223 | int curEvid = getEvid(ind, ind->idose[*endIdx+1]);
| ^~~~~~~
par_solve.cpp: In function ‘void handleSS(int*, int*, double*, double*, double*, double, double, int, int*, int, int*, rx_solving_options*, rx_solving_options_ind*, t_update_inis, void*)’:
par_solve.cpp:1362:39: warning: variable ‘oldI’ set but not used [-Wunused-but-set-variable]
1362 | ei=0, wh, cmt, wh100, whI, wh0, oldI,
| ^~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include/rxode2parseGetTime.h: In function ‘double handleInfusionItem(int, rx_solve*, rx_solving_options*, rx_solving_options_ind*)’:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include/rxode2parseGetTime.h:314:5: warning: ‘infBidx’ may be used uninitialized [-Wmaybe-uninitialized]
314 | if (infBidx == -1) return 0.0;
| ^~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include/rxode2parseGetTime.h:312:9: note: ‘infBidx’ was declared here
312 | int infBidx;
| ^~~~~~~
par_solve.cpp: In function ‘void solveWith1Pt(int*, int*, double*, double*, double*, double, double, int, int*, int, int*, rx_solving_options*, rx_solving_options_ind*, t_update_inis, void*)’:
par_solve.cpp:753:5: warning: ‘idid’ may be used uninitialized [-Wmaybe-uninitialized]
753 | if (idid <= 0) {
| ^~
par_solve.cpp:746:7: note: ‘idid’ was declared here
746 | int idid, itol=0;
| ^~~~
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c prja.c -o prja.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rprintf.c -o rprintf.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c rxData.cpp -o rxData.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c rxInv.cpp -o rxInv.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c rxOptRep.cpp -o rxOptRep.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c rxode2_df.cpp -o rxode2_df.o
In file included from rxode2_df.cpp:33:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include/rxode2parseGetTime.h: In function ‘int handleInfusionStartRm(int*, int*, double*, int*, rx_solve*, rx_solving_options*, rx_solving_options_ind*)’:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include/rxode2parseGetTime.h:223:9: warning: unused variable ‘curEvid’ [-Wunused-variable]
223 | int curEvid = getEvid(ind, ind->idose[*endIdx+1]);
| ^~~~~~~
In function ‘double handleInfusionItem(int, rx_solve*, rx_solving_options*, rx_solving_options_ind*)’,
inlined from ‘double getTime__(int, rx_solving_options_ind*, int)’ at /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include/rxode2parseGetTime.h:381:34:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include/rxode2parseGetTime.h:314:5: warning: ‘infBidx’ may be used uninitialized [-Wmaybe-uninitialized]
314 | if (infBidx == -1) return 0.0;
| ^~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include/rxode2parseGetTime.h: In function ‘double getTime__(int, rx_solving_options_ind*, int)’:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include/rxode2parseGetTime.h:312:9: note: ‘infBidx’ was declared here
312 | int infBidx;
| ^~~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c rxode2parse.cpp -o rxode2parse.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c rxode2random.cpp -o rxode2random.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sbuf.c -o sbuf.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c scaleh.c -o scaleh.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c solsy.c -o solsy.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c stoda.c -o stoda.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c strdup_printf.c -o strdup_printf.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c strncmp.c -o strncmp.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c utilc.c -o utilc.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c utilcpp.cpp -o utilcpp.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PreciseSums/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c vmnorm.c -o vmnorm.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o rxode2.so RcppExports.o approx.o boost.o box.o call_dvode.o cfode.o cfode_static.o common.o corfailure.o correction.o daxpy.o ddot.o dgefa.o dgesl.o dgpadm.o dlsoda.o dop853.o dscal.o dsphiv.o etTran.o expandGrid.o expm.o fnorm.o forder.o handle_evid.o idamax.o init.o intdy.o lsoda.o matexp.o matexp_HM98.o methodswitch.o nearPD.o omegaChol.o opkda2.o orderswitch.o par_solve.o prja.o rprintf.o rxData.o rxInv.o rxOptRep.o rxode2_df.o rxode2parse.o rxode2random.o sbuf.o scaleh.o solsy.o stoda.o strdup_printf.o strncmp.o utilc.o utilcpp.o vmnorm.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpLdTs3U/R.INSTALL2ecac55de2ade2/rxode2/src'
make[1]: Entering directory '/tmp/RtmpLdTs3U/R.INSTALL2ecac55de2ade2/rxode2/src'
make[1]: Leaving directory '/tmp/RtmpLdTs3U/R.INSTALL2ecac55de2ade2/rxode2/src'
installing via 'install.libs.R' to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-rxode2/00new/rxode2
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘rxode2’
finding HTML links ... done
as.ini html
as.model html
as.rxUi html
assertRxUi html
binomProbs html
coef.rxode2 html
dot-assertRenameErrorModelLine html
dot-copyUi html
dot-handleSingleErrTypeNormOrTFoceiBase
html
dot-iniGetAppendArg html
dot-iniHandleAppend html
dot-iniHandleLine html
dot-matchesLangTemplate html
dot-minfo html
dot-modelHandleModelLines html
dot-quoteCallInfoLines html
dot-rxDocTable html
dot-rxGetHiBoundaryPred1AndIni html
dot-rxGetLambdaFromPred1AndIni html
dot-rxGetLowBoundaryPred1AndIni html
dot-rxGetPredictionDVTransform html
dot-rxGetPredictionF html
dot-rxGetPredictionFTransform html
dot-rxGetVarianceForErrorType html
dot-rxIsLinCmt html
dot-rxJacobian html
dot-rxLinCmtGen html
dot-rxPrune html
dot-rxSens html
dot-rxWithOptions html
dot-rxWithSink html
dot-rxWithWd html
dot-useUtf html
erf html
etTrans html
findLhs html
gammap html
gammapDer html
gammapInv html
gammaq html
gammaqInv html
genShinyApp.template html
getBaseIniSimModel html
getBaseSimModel html
getBaseSymengineModel html
getRxThreads html
guide_none html
ini-set html
ini html
is.rxSolve html
llikBeta html
llikBinom html
llikCauchy html
llikChisq html
llikExp html
llikF html
llikGamma html
llikGeom html
llikNbinom html
llikNbinomMu html
llikNorm html
llikPois html
llikT html
llikUnif html
llikWeibull html
logit html
lowergamma html
meanProbs html
model-set html
model html
modelExtract html
odeMethodToInt html
plot.rxSolve html
plus-.rxSolve html
print.rxCoef html
print.rxDll html
print.rxode2 html
probit html
reexports html
rxAllowUnload html
rxAppendModel html
rxAssignControlValue html
rxAssignPtr html
rxBlockZeros html
rxC html
rxCat html
rxChain html
rxChain2 html
rxClean html
rxCombineErrorLines html
rxCompile html
rxCondition html
rxControlUpdateSens html
rxCreateCache html
rxD html
rxDelete html
rxDemoteAddErr html
rxDfdy html
rxDll html
rxDynLoad html
rxDynUnload html
rxErrTypeCombine html
rxExpandFEta_ html
rxExpandGrid html
rxExpandGrid_ html
rxExpandIfElse html
rxExpandSens2_ html
rxExpandSens_ html
rxForget html
rxFun html
rxGetControl html
rxGetDistributionSimulationLines html
rxGetLin html
rxGetModel html
rxGetrxode2 html
rxHtml html
rxIndLinState html
rxIndLinStrategy html
rxIndLin_ html
rxInits html
rxInv html
rxIs html
rxIsCurrent html
rxIsLoaded html
rxLhs html
rxLock html
rxMd5 html
rxModelVars html
rxModels_ html
rxNorm html
rxOptExpr html
rxParams html
rxParseErr html
rxParsePk html
rxParsePred html
rxPkg html
rxPp html
rxPreferredDistributionName html
rxProgress html
rxPrune html
rxReload html
rxRemoveControl html
rxRename html
rxRepR0_ html
rxReservedKeywords html
rxResidualError html
rxS html
rxSetControl html
rxSetCovariateNamesForPiping html
rxSetPipingAuto html
rxSetProd html
rxSetProgressBar html
rxSetSilentErr html
rxSetSum html
rxSetupIni html
rxSetupScale html
rxShiny html
rxSimThetaOmega html
rxSolve html
rxSolveFree html
rxSplitPlusQ html
rxState html
rxSumProdModel html
rxSupportedFuns html
rxSuppressMsg html
rxSymInvChol html
rxSymInvCholCreate html
rxSymInvCholN html
rxSyncOptions html
rxSyntaxFunctions html
rxTempDir html
rxTheme html
rxToSE html
rxTrans html
rxUiDecompress html
rxUiGet html
rxUnloadAll html
rxUse html
rxValidate html
rxVersion html
rxbeta html
rxbinom html
rxcauchy html
rxchisq html
rxexp html
rxf html
rxgamma html
rxgeom html
rxnbinom html
rxnormV html
rxode2-set html
rxode2 html
rxord html
rxpois html
rxt html
rxunif html
rxweibull html
stat_amt html
stat_cens html
summary.rxDll html
summary.rxode2 html
update.rxUi html
uppergamma html
zeroRe html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* creating tarball
packaged installation of ‘rxode2’ as ‘rxode2_2.1.2_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (rxode2)